A couple of things could be involved here:
That setting includes disk space used by any files comprising your website(s) - from the Manage Email Edit page: Limit total disk usage includes web site usage, if any! If you have uploaded a lot of stuff to your website, that can be effecting your quota even if your mailbox is empty.
This may not be relevant, but I mention it as is is a common issue. Assuming you are using POP3 (you said “download the mail”, so I’m assuming you are “popping” it) you need to make sure that any mail that has been moved to your “old-messages” folder is also accounted for. I don’t know how long you have had your account set up or how much mail/spam you get, but, depending upon your settings, a great deal of mail can accumulate here as it is archived (either because there are too many messages in the inbox, or it is “old”).
This is often confusing because that folder is not “subscribed” by default at DreamHost, so many people never look at it! You can subscribe to this folder using the SquirrelMail settings.
This can explain why there is sometimes mail (sometimes a lot* of mail) still “in the mailbox”, but the mailbox appears to be empty.
Finally, if a lot of mail was deleted (or a lot of files were uploaded) an “empty” mailbox may still report it is exceeding quota until the quotas are rechecked - and at DreamHost that happens only once a day. This means you could have a situation where you actually are below quota but the system will not “realized” that until the quotas are again checked (by the next day).